As the retailer liable for sales tax, a marketplace facilitator would generally be responsible for validating exempt transactions. That said, while some marketplaces may have a system to collect and store exemption certificates for tax-exempt transactions, others may not.
The Amazon Tax Exemption Program (ATEP) supports tax-exempt purchases for sales sold by Amazon, its affiliates, and independent third-party sellers that opt to participate in the program. Amazon can also generate transaction-specific exemption certificates that list the actual products ordered, but only if the customer enrolls in the ATEP program in a particular way. ATEP currently doesn’t support partial exemptions.
Amazon advises tax-exempt customers to verify that tax wasn’t collected at checkout. “In some cases,” it explains, “tax may be applied to an order, even if you’re using a tax-exempt account.” This may be because the seller doesn’t participate in Amazon’s tax-exemption program, or because the account doesn’t hold an exemption certificate for a particular state. This list of Amazon’s tax exemption messages gives more examples.
Several other large marketplaces, including Alibaba, eBay and Walmart, have programs for tax-exempt customers. However, smaller or newer marketplaces may not. If you make tax-exempt sales through a marketplace, it’s important to ensure valid exemption certificates are collected, stored, and updated as necessary; if a marketplace isn’t handling sales tax for you, exemption certificate management may fall on you.